This work was partially supported by the Portuguese Fundação para
a Ciência e Tecnologia through POSC and PDTC, namely via:
-
Project grant POSC/EIA/57398/2004: DBYeast: Infrastructures and algorithms for
analysis and identification of gene regulatory networks
-
Project grant PDTC/BIO/56838/2004: Insights into the complex regulatory networks
acting in Yeast cells challenged with drugs/chemical stresses: genome-wide
expression approaches supported by bioinformatics
-
National funds through Programa Operacional Regional de Lisboa 2020, LISBOA-01-0145-FEDER-022231 – the Biodata.pt Research Infrastructure.
The information about Yeast genes other than documented regulations, potential
regulations and the TF binding sites contained in YEASTRACT are gathered from; Saccharomyces
Genome Database (SGD), Gene Ontology (GO) Consortium and Regulatory Sequence Analysis
(RSA) Tools.
We acknowledge SGD for making those file available to the public:
We acknowledge GO Consortium for making GO database and vocabularies freely available
to the public:
- The single OBO format flat file by GO consortium providing ontologies and
terms definitions was parsed to identify level and logical relationships between
the GO terms associated to each gene in the GO hierarchy [3].
http://www.geneontology.org/ontology/gene_ontology.obo
We acknowledge the RSAT team for providing free access to the different functionalities
of the RSA Tools to academic users:
- The Sequence Retrieval functionality provided by RSA Tools was used to retrieve
nucleotide sequences for the genes and promoter sequences for the Yeast genes
[4].
We are grateful to colleagues and friends from the yeast community for their encouragement and suggestions. A very special thanks is due to André Goffeau.
References:
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Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, and Cherry JM.
"Saccharomyces Genome Database"
http://downloads.yeastgenome.org/curation/literature/gene_association.sgd.gz
2. Hong EL, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR,
Fisk DG, Hirschman JE, Livstone MS, Nash R, Oughtred R, Park J, Skrzypek M,
Starr B, Andrada R, Binkley G, Dong Q, Hitz BC, Miyasato S, Schroeder M,
Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, and Cherry JM.
"Saccharomyces Genome Database"
http://downloads.yeastgenome.org/sequence/S288C_reference/orf_protein/orf_trans.fasta.gz
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(2000) Nature Genet. 25: 25-29.
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analysis of yeast regulatory sequences. Yeast 16(2), 177-187.
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